Patch 210831 is available for cryoSPARC v3.2.0

Install, Configure and Update
1

Release Notes

(includes all notes from previous patch 210817)

Added

  • “Reassign Particles to Micrographs” job to reassign particles to their associated micrographs
  • Full Prefix/suffix cutting parameters for matching between input movies and micrographs in
    “Import Micrographs” job
  • Extend master/worker communication timeout with CRYOSPARC_CLIENT_TIMEOUT environment variable

Fixed

  • Exception handling for Clear Intermediate Results
  • Corrected cryosparcm cluster example JSON output

Here’s how to install the patch (cryoSPARC v3.2.0 required):
https://guide.cryosparc.com/setup-configuration-and-management/software-updates#apply-patches

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2

I believe this patch has broken csparc2star.py conversion from CryoSparc to Relion formatting. Please see below:

-bash-4.2$ csparc2star.py --copy-micrograph-coordinates /data/XXX/XXX/XXX/Extract/job005/particles.star cryosparc_P25_J220_014_particles.cs cryosparc_P25_J220_014_particles.star --loglevel debug
Detected CryoSPARC 2+ .cs file
Reading primary file
Assigning parameters 2D classes or single 3D class
Copying image size
Directly copied fields: rlnPhaseShift, ucsfImageIndex, rlnDefocusAngle, rlnSphericalAberration, rlnDefocusV, rlnCtfBfactor, rlnAmplitudeContrast, rlnVoltage, ucsfUid, rlnDefocusU, rlnDetectorPixelSize, ucsfImagePath, rlnOpticsGroup, rlnRandomSubset, rlnOriginX, rlnOriginY, rlnAngleRot, rlnAngleTilt, rlnAnglePsi, rlnClassNumber, rlnImageSize, rlnMagnification
Converting DEFOCUSANGLE from degrees to radians
Converting PHASESHIFT from degrees to radians
Changing RANDOMSUBSET to 1-based index
Changing CLASS to 1-based index
Changing OPTICSGROUP to 1-based index
Converting Rodrigues coordinates to Euler angles
Converted Rodrigues coordinates to Euler angles
/admin/opt/common/sbgrid/programs/x86_64-linux/pyem/20210211/pyem_extlib/pyem-20210211-gqx7/pyem/star.py:536: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
  df[UCSF.IMAGE_INDEX], df[UCSF.IMAGE_PATH] = \
/admin/opt/common/sbgrid/programs/x86_64-linux/pyem/20210211/pyem_extlib/pyem-20210211-gqx7/pyem/star.py:544: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
  df[UCSF.IMAGE_ORIGINAL_INDEX], df[UCSF.IMAGE_ORIGINAL_PATH] = \
Coordinates merge key: None
Traceback (most recent call last):
  File "/programs/x86_64-linux/pyem/20210211/pyem/csparc2star.py", line 120, in <module>
    sys.exit(main(parser.parse_args()))
  File "/programs/x86_64-linux/pyem/20210211/pyem/csparc2star.py", line 71, in main
    df = star.smart_merge(df, coord_star, fields=fields, key=key)
  File "/admin/opt/common/sbgrid/programs/x86_64-linux/pyem/20210211/pyem_extlib/pyem-20210211-gqx7/pyem/star.py", line 146, in smart_merge
    s2 = s2.set_index(key, drop=False)
  File "/programs/x86_64-linux/pyem/20210211/pyem_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/pandas/core/frame.py", line 4555, in set_index
    raise KeyError(f"None of {missing} are in the columns")
KeyError: 'None of [None] are in the columns'
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3

Hi @Navid,

Are you able to send me /data/XXX/XXX/XXX/Extract/job005/particles.star and cryosparc_P25_J220_014_particles.cs to sarulthasan@structura.bio?

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